THE scientific rebel J. Craig Venter created headlines — and drew comparisons to Dr. Frankenstein — when he announced in May that his team had created what, with a bit of stretching, could be called the first synthetic living creature.

Two months later, only a smattering of reporters and local dignitaries bothered to show up at a news conference to hear Dr. Venter talk about a new greenhouse that his company, Synthetic Genomics, had built outside its headquarters here to conduct research.

The contrast in the fanfare reflects the enormous gap between Dr. Venter’s stunning scientific achievements and his business aspirations.

Dr. Venter, now 63, made his name as a gene hunter. He was co-founder of a company, Celera Genomics, that nearly left the federally funded Human Genome Project in the dust in the race to determine the complete sequence of DNA in human chromosomes. He garnered admiration for some path-breaking ideas but also the enmity of some scientific rivals who viewed him as a publicity seeker who was polluting a scientific endeavor with commercialism.

Now Dr. Venter is turning from reading the genetic code to an even more audacious goal: writing it. At Synthetic Genomics, he wants to create living creatures — bacteria, algae or even plants — that are designed from the DNA up to carry out industrial tasks and displace the fuels and chemicals that are now made from fossil fuels.

“Designing and building synthetic cells will be the basis of a new industrial revolution,” Dr. Venter says. “The goal is to replace the entire petrochemical industry.”

His star power has attracted $110 million in investment so far, in addition to hundreds of millions of dollars in research financing, making Synthetic Genomics among the wealthiest companies in the new field known as synthetic biology. “If you think of an iconic, Steve Jobs character in the life sciences field, he comes to mind,” says Steve Jurvetson of the venture capital firm Draper Fisher Jurvetson, which invested in Synthetic Genomics.

But the path is long, with no guarantee of success. And as with DNA sequencing, Dr. Venter is stirring some unease in the synthetic biology field. Some competitors say designing entire cells is too far-fetched and that less flashy companies are ahead of Synthetic Genomics.

“I don’t know how many decades his funders have given him,” says Jay Keasling, co-founder of Amyris Inc., which is trying to produce biofuels and a malaria drug by modifying existing organisms, not by creating entirely new ones.

Moreover, Dr. Venter’s track record as a businessman is mixed. While Celera succeeded in sequencing the human genome, it failed to make a business of selling the genomic data, and Dr. Venter was fired by the president of Celera’s parent company, with whom he had had many disagreements.

What really drives him, Dr. Venter and those close to him say, is the desire for scientific accomplishments, publications and recognition, and for the Nobel Prize that still eludes him. Business is just a means to a scientific end.

“Craig is just a hopeless businessman,” Alan G. Walton, a venture capitalist and a friend of Dr. Venter, says only half-jokingly.

Yet Dr. Venter has a history of defying skeptics, and many people are betting that he will succeed this time as well. Dr. Walton, in fact, invested personally in Synthetic Genomics, and his venture firm, Oxford Bioscience Partners, recently wanted to sink a hefty sum into the company but was turned down when Dr. Venter found other investors offering better terms.

Exxon Mobil is giving Synthetic Genomics $300 million in research financing to design algae that could be used to produce gasoline and diesel fuel. (The new greenhouse will be used for that research.)

BP has invested in the company itself, turning to Synthetic Genomics to study microbes that might help turn coal deposits into cleaner-burning natural gas. Another investor, the Malaysian conglomerate Genting, wants to improve oil output from its palm tree plantations, working toward what its chief executive calls a “gasoline tree.”

And in a deal expected to be announced this week, the pharmaceutical giant Novartis will work with Dr. Venter to synthesize influenza virus strains as a potentially faster way to make flu vaccines.

Synthetic Genomics is also exploring the use of algae to produce food oils and, possibly, other edible products.

Dr. Venter muses, “What if we can make algae taste like beef?”

SCIENTISTS have long been able to insert foreign genes into organisms. Human insulin is manufactured for diabetics by bacteria containing the human insulin gene. Bacterial genes are put into corn plants to give them resistance to herbicides and insects.

But until now, genetic engineering has been mainly a process of cutting and pasting a gene from one organism to another. Only one or a few genes are spliced into a cell, and considerable trial and error is required before a gene functions properly in its new host.

Synthetic biology aims to allow more extensive changes, and in a more efficient and predictable way. That would make engineering a cell more like designing a bridge or a computer chip, enabling biologists to put prefabricated components together in different combinations.

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In the approach toward which Dr. Venter is driving, engineers would specify the entire genetic code of a cell — essentially the software that runs the cell — on computers, making design changes as if on a word processor. They would then press the “print” button, so to speak, and the DNA would be manufactured from its chemical components. The synthetic DNA would then be transplanted into an existing cell, where it would “boot up” and take control of the cell’s operations.

This is essentially what Dr. Venter’s team announced in May. It synthesized the million-letter genome of a simple bacterium, the longest synthetic piece of DNA produced so far, and transplanted it into a slightly different type of bacterium, which then began to replicate. A critic called the synthetic creature Synthia, a name that has started to stick.

Reaction was swift. “We heard from the pope and the president the same day,” Dr. Venter said.

President Obama immediately asked his bioethics commission to examine the potential benefits and risks of synthetic biology. The main concerns are bio-terror and bio-error — the deliberate or inadvertent creation of organisms that are toxic or ecologically harmful. The president’s action seemed to confirm concerns in the field that Dr. Venter’s bold claims would stir public fear and lead to burdensome regulation. “The only regulation we need is of my colleague’s mouth,” says Dr. Keasling of Amyris.

The Vatican, somewhat surprisingly, cautiously praised the work as a potential way of treating diseases, saying it did not regard the synthesis of DNA as the creation of life.

Dr. Venter concedes that he was not creating life from scratch, because an existing cell was used to house the synthetic DNA. But he argues that it was still accurate to call this a synthetic cell. Because the synthetic DNA took control of producing the cell’s components, replicated cells would gradually lose characteristics of the original host cell. Dr. Venter says that he has long supported and paid for research into the ethics and regulation of the field and that there should be restrictions on letting synthetic cells loose in the environment.

Regardless of the work’s ethical implications, some experts say it will have limited industrial use. Synthia’s creation took 15 years and cost $40 million. The synthetic bacterium is not robust enough for industrial production of chemicals. Most important, the synthetic genome was nearly a replica of the genome from an existing bacterium. The truth is, scientists do not yet know enough to design a genome from scratch.

Even if they could, it would be overkill, says George Church, a Harvard genetics researcher who has helped start two companies that are modifying organisms to produce fuel. He says that only a few genetic changes are needed.

“One of the things that is missing,” he says of Dr. Venter’s work, “is a clear articulation of why you would want to change the whole genome.”

Dr. Venter says his company will use more limited genetic engineering for its first algae-based biofuels. But he says the ability to synthesize DNA is improving rapidly. And while the first synthetic genome had “plagiarized nature,” he says scientists will eventually learn how to design genomes.

Exxon is also hopeful the technique will be useful.

“It can be applied to Synthia or it can be applied to biofuels,” says Emil Jacobs, a top research executive at Exxon, who says that it will nonetheless take years and billions of dollars before algae will be producing meaningful amounts of fuel.

AN indifferent student in his youth, Dr. Venter spent his time surfing and skirt-chasing, according to his 2007 autobiography, “A Life Decoded.” But harrowing experiences as a medic in the Vietnam War instilled in him a sense of purpose. After returning from Vietnam, he progressed rapidly from community college to a doctorate in physiology and pharmacology from the University of California, San Diego. Eventually, he joined the National Institutes of Health, where he developed a way to find genes without waiting for the genome to be sequenced. In 1992, venture capitalists set up a new company, Human Genome Sciences, to commercialize the technology. But Dr. Venter, reluctant to give up academic freedom, did not join the business, instead starting a nonprofit research institute that supplied data to the company. The arrangement fell apart after a few years.

Then came his up-and-down experience with Celera. It was later revealed that the genome it had sequenced was mainly Dr. Venter’s own.

He came away from the experience wealthy. He estimates that his net worth is in the tens of millions of dollars, even after giving more than $100 million in Human Genome Sciences and Celera stock to endow his research organization, which is now called the J. Craig Venter Institute.

He has a 5,000-square-foot house overlooking the Pacific, a 95-foot yacht, a Tesla electric car, fancy motorcycles and other toys to satisfy a lust for adventure that is as outsize as his lust for science.

Dr. Venter said he started Synthetic Genomics in 2005 mainly to fund the research on the synthetic cell.

“I think it’s comical that I keep being referred to as a businessman,” he said. “What I’ve been successful in is finding alternate ways to fund research.”

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Hamilton Smith, his longtime research partner and a Nobel laureate, co-founded Synthetic Genomics with Mr. Venter. Also involved were two friends who are now directors of the company: David Kiernan, a Washington lawyer whom Dr. Venter met through sailing, and Juan Enriquez, who was an international affairs researcher at Harvard until meeting Dr. Venter at a New Year’s gathering 15 years ago.

“I saw this guy sitting off in a corner by himself,” Mr. Enriquez says. “I went and talked to him and disappeared on my wife for the rest of the evening.” Mr. Enriquez changed the focus of his research to life sciences and started a venture capital firm that participated in the first $30 million round of investment in Synthetic Genomics. Half of that $30 million came from Alfonso Romo Garza, a Mexican industrialist.

Two other rounds followed. As part of the most recent round, Life Technologies, a leading manufacturer of laboratory equipment and chemicals, invested $15 million for a 2.9 percent stake, giving Synthetic Genomics an imputed valuation of over $500 million.

Dr. Venter says he now owns about 15 percent of the company. The Malaysian conglomerate and its chief executive, K. T. Lim, together own nearly 20 percent, making them the largest holders, Dr. Venter says.

Synthetic Genomics has about 130 employees. But much of its research, including the development of the synthetic cell, is done at the J. Craig Venter Institute. Synthetic Genomics pays for about 25 of the institute’s roughly 300 researchers, and has rights to their results. The rest of the institute’s funding comes mainly from federal grants and its endowment. Dr. Venter, who turns 64 in October, has not worked directly with test tubes or gene sequencers for decades. He only charts the course and steers.

“He knows exactly what we’re doing every day,” says Dr. Smith, who still does work in the lab. “Craig tends to come in when things get stalled and points us in the right direction.”

Mr. Romo, who is on the board of Synthetic Genomics, says the number of deals the company has negotiated “is proof that he is a good manager.”

Still, there have been efforts to install a No. 2 person to handle day-to-day business. That has not proved easy. Joel McComb, a General Electric veteran, served as chief operating officer for only a few months this year. Aristides Patrinos, a former Department of Energy official who is president of Synthetic Genomics, works mostly on government affairs.

FOR now, Dr. Venter is where he wants to be. With most of the company’s money coming from corporate partners rather than from impatient venture capitalists, he says he is under less pressure to deliver in the short term. And he says he is in greater control of his own destiny than in previous business ventures.

“Science is the business right now,” he said. “If the science works, the business works, and vice versa.”

NASA scientist finds 'alien life' fossilsRichard Hoover's paper, along with pictures of the microscopic earthworm-like creatures, were published late Friday in the peer-reviewed Journal of Cosmology, which is available free online.Hoover sliced open fragments of several types of carbonaceous chondrite meteorites, which can contain relatively high levels of water and organic materials, and looked inside with a powerful microscope.He found bacteria-like creatures that he calls "indigenous fossils," which he believes originated beyond Earth and were not introduced here after the meteorites landed."He concludes these fossilized bacteria are not Earthly contaminants but are the fossilized remains of living organisms which lived in the parent bodies of these meteors, e.g. comets, moons, and other astral bodies," said the study."The implications are that life is everywhere, and that life on Earth may have come from other planets."Studies that suggest alien microbes can be contained in meteorites are not new, and have drawn hefty debate over how such life could survive in space and how and where life may have originated in the universe.The journal's editor in chief, Rudy Schild of the Center for Astrophysics, Harvard-Smithsonian, said Hoover is a "highly respected scientist and astrobiologist with a prestigious record of accomplishment at NASA.""Given the controversial nature of his discovery, we have invited 100 experts and have issued a general invitation to over 5,000 scientists from the scientific community to review the paper and to offer their critical analysis," he said.Those commentaries will be published March 7 through March 10.A NASA-funded study in December suggested that a previously unknown form of bacterium had been found deep in a California lake that could thrive on arsenic, adding a new element to what scientists have long considered the six building blocks of life.That study drew plenty of criticism, particularly after NASA touted the announcement as evidence of extraterrestrial life. Scientists are currently attempting to replicate those findings

Fuel From BacteriaPublished by Steven Novella under Technology Comments: 25We are used to thinking of bacteria as germs – something to be shunned. In fact, the vast majority of bacteria species are indifferent to humans – they are neither helpful nor harmful. A small minority of species are pathogenic, capable of infecting humans and causing harm. And a small number of species live symbiotically with humans. We all carry an ecosystem of about 100 bacteria species in and on us.With genetic engineering technology we have also created a fourth category of bacteria – those that can be used as microscopic factories. For years we have been using bacteria to cheaply manufacture drugs and other compounds. Just insert the gene for human insulin in the right place, and the little buggers start cranking it out.Researchers are exploring the use of genetically engineered bacteria for other uses as well. For example, bacteria have been shown to secrete nanotubes, and can potentially be used for microelectronics.But the potential application that seems to be getting the most press attention is making biofuels from bacteria. Bacteria can function to digest a biofuel crop, like switch grass, typically breaking down the cellulose so that it can be processed into ethanol. But a potentially superior approach would be to have bacteria produce fuel directly. Because the direct method avoids potentially expensive steps, it is likely to be more cost-effective, which is critical for the adoption of any alternative fuel.There are frequent news items claiming breakthroughs in this technology, but two I want to mention specifically. Here’s the first.The findings, reported online in the journal Applied and Environmental Microbiology, mark an important advance in the production of normal butanol, or n-butanol, a four-carbon chain alcohol that has been shown to work well with existing energy infrastructure, including in vehicles designed for gasoline, without modifications that would be required with other biofuels.They achieved this with a modified version of the common bacterium, E. coli.A second team announced a few weeks ago that they modified a cyanobacterium to produce diesel fuel or ethanol.These are both exciting breakthroughs – bacteria essentially can thrive on waste and sunshine and produce biofuel. They fix carbon from the atmosphere, which then gets released upon burning, so such biofuels would be carbon neutral (the same is not true of some crop-based biofuels where the crops are fertilized with petrochemical-based fertilizer).I have actually been reading about claimed breakthroughs with bacteria to fuel technology for a few years. This is one of those future technology news items that is hard to know if it will pan out, and how soon. Is this a hand-held computer or jetpack? It seems that there are non-trivial technical hurdles to overcome, mostly involved with scaling up the production. It’s one thing to make diesel fuel in some small test containers, another to run a massive factory generating millions of gallons. If the process can’t scale up, we won’t ever be pumping it into our cars.What is clear is that engineered bacteria are already a proven technology, and I think it’s probable that they will be increasingly used in the future. Beyond being microfactories, researchers are exploring the use of engineered bacteria to augment the bacterial flora of our bodies, with potential health benefits.But predicting any particular application is difficult. I think the chances are good for biofuel from bacteria, and I certainly hope this technology pans out. But it remains to be seen.

Why Math WorksIs math invented or discovered? A leading astrophysicist suggests that the answer to the millennia-old question is both

By Mario Livio | August 3, 2011 | 3 Share Email Print Fractals, such as this stack of spheres created using 3-D modeling software, are one of the mathematical structures that were invented for abstract reasons yet manage to capture reality.

Image: Illustration by Tom Beddard

In BriefThe deepest mysteries are often the things we take for granted. Most people never think twice about the fact that scientists use mathematics to describe and explain the world. But why should that be the case? Math concepts developed for purely abstract reasons turn out to explain real phenomena. Their utility, as physicist Eugene Wigner once wrote, “is a wonderful gift which we neither understand nor deserve.” Part of the puzzle is the question of whether mathematics is an invention (a creation of the human mind) or a discovery (something that exists independently of us). The author suggests it is both.

Most of us take it for granted that math works—that scientists can devise formulas to describe subatomic events or that engineers can calculate paths for space­craft. We accept the view, initially espoused by Galileo, that mathematics is the language of science and expect that its grammar explains experimental results and even predicts novel phenomena. The power of mathematics, though, is nothing short of astonishing. Consider, for example, Scottish physicist James Clerk Maxwell’s famed equations: not only do these four expressions summarize all that was known of electromagnetism in the 1860s, they also anticipated the existence of radio waves two decades before German physicist Heinrich Hertz detected them. Very few languages are as effective, able to articulate volumes’ worth of material so succinctly and with such precision. Albert Einstein pondered, “How is it possible that mathematics, a product of human thought that is independent of experience, fits so excellently the objects of physical reality?”

As a working theoretical astrophysicist, I encounter the seemingly “unreasonable effectiveness of math­ematics,” as Nobel laureate physicist Eugene Wigner called it in 1960, in every step of my job. Whether I am struggling to understand which progenitor systems produce the stellar explosions known as type Ia supernovae or calculating the fate of Earth when our sun ultimately becomes a red giant, the tools I use and the models I develop are mathematical. The uncanny way that math captures the natural world has fascinated me throughout my career, and about 10 years ago I resolved to look into the issue more deeply.

I'm not a mathematician, but I can tell you what my math instructor said about this topic. His opinion was that math isn't the study of truth, but the study of implication. He believes math was invented from the ground up to provide useful models, and that we designed it to work the way it does.

The reason for that is because there are equations that use things like (n)! as a multiplier and have a coefficient as its first term when n! = 0!. They want to keep the first term instead of zeroing it out, so they just made up the definition of 0! = 1. There isn't any truth there. It was invented for our use. Beyond that, it has broader implications in mathematics which weren't necessarily intended. According to him, all math is like that. Yes, math builds models, but only because we crafted the system to work for us that way.

updated 52 minutes ago 2011-08-02T19:28:13 Font: +-Researchers have constructed an invisibility cloak capable of hiding a tiny object by altering the behavior of the light that hits it. This is the first invisibility cloak made out of sophisticated, artificial materials called metamaterials that work with the full spectrum of light visible to the human eye.

The cloak the researchers constructed and tested could disguise a miniscule object, 0.000024 inches wide by 0.000012 inches high — roughly the size of a red blood cell or 100 times thinner than a human hair, according to study researcher Majid Gharghi, a postdoctoral fellow at the University of California, Berkeley.

Until now, metamaterial cloaks such as this one have hidden objects only from limited parts of the electromagnetic spectrum, outside the range of what we can see or for only part of the visible range. And another type of device, made of calcite crystal prisms, has been used to hide things in white, or full-spectrum, light, but only if wavelengths of that light are traveling at a particular angle, or are properly polarized.

The cloak, which works for the full spectrum of visible light traveling at any angle, is made out of silicon nitride layered on top of silicon oxide with minute pores. The silicon nitride is etched with a special pattern of holes. Because of their carefully calculated size, these holes can alter the speed at which light travels through the layer that contains them. This allows the engineers to manipulate our ability to see things.

"What you see is actually not just the light; what you are seeing is how the light is interacting with its environment," said Chris Gladden, a graduate student in Xiang Zhang's group at UC Berkeley, where the work was done.

The pattern of microscopic holes essentially reconstructs the reflected light as if the light never hit the object in the first place, fooling the eye into missing the object.

In theory, at least, this approach could be used to cloak much larger objects.

"The problem becomes actually making a cloak that big. The cloak Majid and I created consists of about 7,000 holes," Gladden said.

It takes about a week to construct a microscopic cloak like this. While the cloak could be scaled up, eventually the time required would make the project impossible, they said. However, some techniques being developed might reduce that time.

Another logistical issue: The cloak must be much larger than the object it covers. Nevertheless, this cloak is a step forward in invisibility technology. The research appears in the journal Nano Letters.

I can't say that I have a good grasp of the internal workings of the NSF's grant process and the degree of political graft that may or may not be involved in the awarding of said grants, however given the abuses well documented under this administration and our dire economic condition, I'm wanting the USG out of the grant business altogether.

This, admittedly, does not address the manner in which NSF grants are awarded. Here is a list, of 577, of NSF funded findings. I think some of them may be of interest.

I can't say that I have a good grasp of the internal workings of the NSF's grant process and the degree of political graft that may or may not be involved in the awarding of said grants, however given the abuses well documented under this administration and our dire economic condition, I'm wanting the USG out of the grant business altogether.

This, admittedly, does not address the manner in which NSF grants are awarded. Here is a list, of 577, of NSF funded findings. I think some of them may be of interest.

I don't know, but there is good to come out of the NSF grants. There is also the possibility that there will be discoveries that benefit the long term longevity of the species that are not prone to business interests, which tend to be more short term, nbottom line in orientation. The astronomical discoveries, for example.

I can't say that I have a good grasp of the internal workings of the NSF's grant process and the degree of political graft that may or may not be involved in the awarding of said grants, however given the abuses well documented under this administration and our dire economic condition, I'm wanting the USG out of the grant business altogether.

This, admittedly, does not address the manner in which NSF grants are awarded. Here is a list, of 577, of NSF funded findings. I think some of them may be of interest.

I don't know, but there is good to come out of the NSF grants. There is also the possibility that there will be discoveries that benefit the long term longevity of the species that are not prone to business interests, which tend to be more short term, nbottom line in orientation. The astronomical discoveries, for example.

I can't say that I have a good grasp of the internal workings of the NSF's grant process and the degree of political graft that may or may not be involved in the awarding of said grants, however given the abuses well documented under this administration and our dire economic condition, I'm wanting the USG out of the grant business altogether.

This, admittedly, does not address the manner in which NSF grants are awarded. Here is a list, of 577, of NSF funded findings. I think some of them may be of interest.

Did you see my post that said "[t]here is also the possibility that there will be discoveries that benefit the long term longevity of the species that are not prone to business interests, which tend to be more short term, nbottom line in orientation. The astronomical discoveries, for example."

Did you see my post that said "[t]here is also the possibility that there will be discoveries that benefit the long term longevity of the species that are not prone to business interests, which tend to be more short term, nbottom line in orientation. The astronomical discoveries, for example."

The days of thinking of time as a river—evenly flowing, always advancing—are over. Time perception, just like vision, is a construction of the brain and is shockingly easy to manipulate experimentally. We all know about optical illusions, in which things appear different from how they really are; less well known is the world of temporal illusions. When you begin to look for temporal illusions, they appear everywhere. In the movie theater, you perceive a series of static images as a smoothly flowing scene. Or perhaps you've noticed when glancing at a clock that the second hand sometimes appears to take longer than normal to move to its next position—as though the clock were momentarily frozen.

Serge Haroche and David J. Wineland have independently invented and developed methods for measuring and manipulating individual particles while preserving their quantum-mechanical nature, in ways that were previously thought unattainable.

The Nobel Laureates have opened the door to a new era of experimentation with quantum physics by demonstrating the direct observation of individual quantum particles without destroying them. For single particles of light or matter the laws of classical physics cease to apply and quantum physics takes over. But single particles are not easily isolated from their surrounding environment and they lose their mysterious quantum properties as soon as they interact with the outside world. Thus many seemingly bizarre phenomena predicted by quantum physics could not be directly observed, and researchers could only carry out thought experiments that might in principle manifest these bizarre phenomena.

Through their ingenious laboratory methods Haroche and Wineland together with their research groups have managed to measure and control very fragile quantum states, which were previously thought inaccessible for direct observation. The new methods allow them to examine, control and count the particles.

Their methods have many things in common. David Wineland traps electrically charged atoms, or ions, controlling and measuring them with light, or photons.

Serge Haroche takes the opposite approach: he controls and measures trapped photons, or particles of light, by sending atoms through a trap.

Both Laureates work in the field of quantum optics studying the fundamental interaction between light and matter, a field which has seen considerable progress since the mid-1980s. Their ground-breaking methods have enabled this field of research to take the very first steps towards building a new type of super fast computer based on quantum physics. Perhaps the quantum computer will change our everyday lives in this century in the same radical way as the classical computer did in the last century. The research has also led to the construction of extremely precise clocks that could become the future basis for a new standard of time, with more than hundred-fold greater precision than present-day caesium clocks.

Mother Nature, Version 2.0 Welcome to the world of synthetic biology, where micro-organisms can be programmed to invade and destroy cancer cells..By SCOTT GOTTLIEB

It once seemed that the most profound feats stemming from DNA-based science would spring from our ability to read and detect genes, which we call the science of genomics. But the real opportunities lie in our ability to write DNA, to synthesize new gene sequences and insert them into organisms, resulting in brand-new biological functions. Printing novel DNA might open the way to achievements once only conceivable in science fiction: designer bacteria that can produce new chemicals, such as more efficient fuels, or synthetic versions of our cells that make us resistant to the effects of radiation.

The first such genome was made in 2000 in an experiment where scientists synthesized their own version of the hepatitis C virus so that they could alter it and discover a way to disable the infection. Today it is possible to read gene sequences into computers, where we can alter them and then print a modified gene into living cells. In "Regenesis," a book exploring the science of synthetic biology, George Church and Ed Regis imagine a world where micro-organisms are capable of producing clean petroleum or detecting arsenic in drinking water, where people sport genetic modifications that render their bodies impervious to the flu, or where a synthetic organism can be programmed to invade and destroy cancer cells.

Mr. Church is currently a professor of genetics at the Harvard Medical School. He arrived there after a storied career as one of the early pioneers in the science of identifying and reading genes. With fellow scientist Walter Gilbert, he developed the first consistent process for sequencing strands of DNA and, in 1984, helped launch the historic project to map the entire human genome while he was a research scientist at the then newly formed biotech company Biogen.

"Regenesis" begins with a historical look at the evolution of genomics, providing a primer on the science that underlies the field. The authors then describe the ways in which different applications of synthetic biology may transform established science and effectively make obsolete current principles in medicine and manufacturing. Along the way, they offer a definitive account of the advances and business ventures that define this new science.

Mr. Church and Mr. Regis, a broadly published science writer, spend a lot of time describing the latest industrial applications of synthetic genomics. For example, researchers are using genetically altered cyanobacteria to convert sunlight and carbon dioxide into alkanes, the molecular constituents of diesel fuel. This green science isn't yet cost effective. When the Navy recently bought 21,000 gallons of algae-derived jet fuel, it cost $424 per gallon. (Currently, the oil-derived fuel costs around $5 per gallon.) But the ability to alter organisms to increase their yield is growing at an exponential tempo. And our ability to manipulate DNA sequences on microprocessors and write the strands into living organisms is taking a similar trajectory. As the tools for doing these things become more powerful, industrial exploitation will become more widespread and effective.

Then there is the multiplex automated genetic engineering machine invented by Mr. Church and three colleagues from Harvard. This tool makes the process of synthesizing new genes much faster. One of the most promising, although controversial, applications is to re-engineer the human genome itself "for the purpose of preventing many diseases from occurring in the first place." The tool holds great promise. Imagine if we could remove from our genomes the "host machinery" that viruses need to replicate, potentially making us immune to illnesses as ordinary as the flu.

Such developments promise a great deal, but they also make people uncomfortable and prompt calls for limits on what scientists are allowed to do. But recent history suggests that, when new scientific developments have created theoretical risks, scientists themselves have come together to set boundaries on their work until any uncertainties can be better understood and resolved. The self-imposed limits have also made sure that new science wasn't used in dangerous or untoward ways. When there were concerns about recombinant DNA in the early days of synthetic biology, for example, researchers imposed a moratorium until the risks could be contained. When gene therapy was believed to harbor latent risks, research was largely put on hold until the risks were better understood. Sometimes, the theoretical risks have led to a principle of absolutist precaution that impedes progress. Today the Food and Drug Administration so tightly regulates gene therapy that few new ventures go forward. But, Messrs. Church and Regis argue, the practical promise of a technology will ultimately prevail. "The industrial revolution that the Luddites tried to prevent in 1811 has brought us enormous benefits," they write.

The more elusive problem isn't safety but security—"preventing the deliberate misuse of engineered organisms," as the authors define the concept. DNA synthesizers are small, cheap and easy to procure. The technical means for harnessing these tools is relatively straightforward—within the grasp of scientists of modest training. The instruction sets are also easily found on the Internet. Rogue regimes and lone villains could one day exploit these scientific methods for diabolical aims. Such a security breach could play like the plot of the 1995 hit film "Twelve Monkeys," where a wicked scientist engineers a virus that nearly drives mankind to extinction. With the advent of what the authors call "garage biology," Messrs. Church and Regis think, such scenarios are no longer wildly implausible. "In the end, we found no magic bullets for absolutely preventing worst-case scenarios, no fail-safe fail-safes."

Many point to the Internet as the defining technology of our age. When history is written centuries from now, it is more likely that writing DNA will be the most enduring innovation, so long as we keep it in safe hands.

Dr. Gottlieb is a physician and a resident fellow at the American Enterprise Institute

A Mississippi baby born with the AIDS virus appears to have been cured after being treated with an aggressive regimen of drugs just after her birth 2½ years ago, an unusual case that could trigger changes in care for hundreds of thousands of babies born globally each year with HIV.

The findings, reported Sunday by researchers, mark only the second documented case of a patient being cured of infection with the human immune-deficiency virus. The first, an adult man known as the Berlin patient, was cured as a result of a 2007 bone-marrow transplant.

A newfound particle discovered at the world's largest atom smasher last year is, indeed, the Higgs boson, the particle thought to explain how other particles get their mass, scientists reported today (March 14) at the annual Rencontres de Moriond conference in Italy.

Physicists announced on July 4, 2012, that, with more than 99 percent certainty, they had found a new elementary particle weighing about 126 times the mass of the proton that was likely the long-sought Higgs boson. The Higgs is sometimes referred to as the "God particle," to the chagrin of many scientists, who prefer its official name.

Born without a penis, 39-year-old Andrew Wardle will soon undergo surgery to create a functioning organ using skin and tissue from his arm.

By Erin Hicks, Everyday Health Staff Writer

WEDNESDAY, March 20, 2013 — A British man born without a penis is preparing to go under the knife in a surgery that would create a functioning penis using skin and tissue taken from his arm.

Andrew Wardle, a 39-year-old from London, was born with testicles but without a penis, and with an ectopic bladder, meaning it formed outside his body, according to The Sun.

Growing up, he had kidney problems and infections, and underwent 15 operations to build a tube from his bladder so he could urinate.

“I never thought this day would come, and I still can’t believe it is possible for me to actually have a fully functioning penis,” Wardle told The Sun.

Surgery to construct a penis has been done in the United States, but is not common, said Christopher M. Gonzalez, MD, professor of urology at Northwestern University in Evanston, Ill.

“There are people here [in the United States] more than capable of doing [this type of procedure]. We do a lot of reconstructive work, but we don’t see a lot of people with this type of surgery,” said Dr. Gonzalez.

How Penis Reconstruction Surgery Works

Gonzalez explained that the surgery, called a forearm free-flap procedure, involves taking a piece of tissue from the inside of the forearm, as well as the radial artery that runs along the forearm. The artery can be put in place in the area underneath the scrotum to provide blood supply, then the tissue, muscle, and skin from the forearm can be formed into a penis.

There are a few potentially serious complications from the surgery. The skin could die or the tissue could refuse to take, for example. Rarely, blood clots could occur, Gonzalez said. Some patients have permanent scars on their arm from which the tissue was taken, but for the most part there aren’t many complaints from patients about scarring, he added.

Wardle is opting for an additional surgery to build a tube from his bladder so he could urinate normally, though there are other options, said Gonzalez. One is to to create a hole under the scrotum from which a man could urinate.

Additional procedures could be done so the reconstructed penis could ejaculate, and even become erect. For ejaculation to be possible, a surgeon could form a tube inside the flap to create a urethra from the prostate, Gonzalez said.

Sex Life After Surgery?

If you’re wondering whether a person who has had penis reconstruction surgery can have an erection and be sexually intimate with a partner, the answer is yes, but it’ll take more than Viagra. While many men who have had such surgery have feeling in their reconstructed penises, the tissue that's used to form the penis — like that from the forearm — lacks erectile tissue. Therefore, having an erection would require some type of prosthesis.

“You have two options: A malleable penile prosthesis, which involves a couple of cylinders in the penis you would bend up or down when you want it to become erect, or an inflatable prosthesis that fills with saline that you could pump and then deflate when you don’t want an erection,” said Gonzalez.

Like Sex Change Surgery

The reconstructive surgery Wardle is undergoing is the same that a female would face if she wanted to become a male, said Gonzalez. “For women who want sex changes, this is what they would do,” he said.

Penis reconstruction surgery isn’t common because there aren’t many men born with Wardle’s rare condition. Other candidates for this type of surgery: Men needing construction after penile cancer, or someone who had a traumatic accident and had their penis amputated. “We see that once in a while, but it’s pretty rare,” Gonzalez said.

Wardle is an ideal patient for this type of surgery, according to Gonzalez, because he’s older and can deal with the psychological issues that come along with the surgery.

“I think he is a good index patient for something like this,” Gonzalez said. “With proper psychological counseling, I think he would certainly benefit.”

Last Updated: 03/20/2013

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"A good stickgrappler has good stick skills, good grappling, and good stickgrappling and can keep track of all three simultaneously. This is a good trick and can be quite effective." - Marc "Crafty Dog" Denny

By PAUL G. ALLEN And FRANCIS S. COLLINS In science there are moments when prior discoveries, advances in technology, and visionary leadership align to create the opportunity for a great leap. It happened in 1961, when President Kennedy called for a new era of space exploration, which took Americans to the moon. It happened again in 1990, when the Department of Energy and the National Institutes of Health transformed the future of biomedical research by launching the Human Genome Project.

The timing is perfect now for a federally coordinated effort to unlock the secrets of the brain, in line with President Obama's call this month for an ambitious project to map the most complex organ in the known universe.

This is a watershed moment. The goal is to revolutionize how we study the brain, and to gain powerful insights into neurological diseases and mental-health disorders. It is past time to solve questions with profound implications for tens of millions who will benefit from treatments for depression, Parkinson's disease, Alzheimer's, autism and many other disorders.

Though the two of us have rowed in different waters, we share a longtime fascination with the brain. It is what makes us who we are and defines both our individuality and common humanity. Over the past several decades, the scientific community has begun to decipher the brain's intricate language. New, noninvasive tools like optogenetics and calcium imaging enable us to see and manipulate the brain at the molecular level. Recent advances in three-dimensional, ultra-high-resolution microscopy reveal which nerve cells switch on in a particular circuit.

A new era of information technology allows us to build out super-data sets to track and organize these intercellular connections. With the aid of large-scale computer resources, we understand enough about the physics of the brain—in essence, a piece of highly excitable matter—to begin to simulate complete nervous systems.

Freely available mapping tools, such as those developed at the Allen Institute for Brain Science, along with the National Institutes of Health's Human Connectome project and other open-access databases, have accelerated research around the world. As a result, we can now define the functional geography of the cerebral cortex, the region that gives rise to perception, consciousness, language, reasoning and memory.

While neuroscientists have learned a lot, critical pieces regarding the brain's code for processing, storing and retrieving information are still missing. Neuroscience today is like chemistry before the periodic table: People knew about elements and compounds but lacked a systematic theory to classify their knowledge.

Today we know that neurons fire and we know that they are connected. We don't know how they act in concert to govern behavior, the essential question in treating neurological disease and mental-health disorders. Most of all, we have a limited understanding of how the brain translates its rich sensory experiences into complex mental states and behaviors, all at the speed of thought.

Big problems demand big solutions. The human brain contains nearly 100 billion neurons of at least a thousand distinct varieties. Those nerve cells make at least 100 trillion connections. No single discovery, no one researcher, will be able to crack the brain's code. The next generation of neuroscience breakthroughs will emerge from collaboration among a range of disciplines, from physics and biology to nanoscience, computer science and engineering. All hands must be on deck.

Progress will also hinge on the cooperation of the public and private sectors, a welcome aspect of the president's "BRAIN" initiative. We'll need creative, nimble management to ensure the best work out of both sides. The private realm, in particular, will require encouragement to play its role. For scientific leadership, the federal effort must tap into the brightest minds in the field.

It is our view that tough fiscal times demand creative approaches and more innovation. As President Obama has noted, the Human Genome Project has returned $140 in economic growth and new industry for every government dollar invested. We are confident that the BRAIN initiative will pay comparable dividends over time, and ultimately boost social productivity, reduce health-care costs and alleviate untold suffering. All humanity will benefit.

Mr. Allen, who cofounded Microsoft in 1975, is chairman of Vulcan Inc. and founder of the Allen Institute for Brain Science. Dr. Collins is director of the National Institutes of Health. MSFT +1.71%

Not sure where exactly this would fit, science was the best I could think of.

While preparing for an IT certification there is a small section within the Encryption chapter that mentions the Jefferson Disk, yes it is the same person that is one of our forefathers.

First invented by Thomas Jefferson in 1795, this cipher did not become well-known and was independently invented by Commandant Etienne Bazeries, the conqueror of the Great Cipher, a century later. The system was used by the United States Army from 1923 until 1942 as the M-94.

The Jefferson disk, or wheel cypher as Thomas Jefferson named it, also known as the Bazeries Cylinder, is a cipher system using a set of wheels or disks, each with the 26 letters of the alphabet arranged around their edge. The order of the letters is different for each disk and is usually scrambled in some random way. Each disk is marked with a unique number. A hole in the centre of the disks allows them to be stacked on an axle. The disks are removable and can be mounted on the axle in any order desired. The order of the disks is the cipher key, and both sender and receiver must arrange the disks in the same predefined order. Jefferson's device had 36 disks. [Kahn, p. 194]

For more than 200 years, buried deep within Thomas Jefferson's correspondence and papers, there lay a mysterious cipher -- a coded message that appears to have remained unsolved. Until now.

The cryptic message was sent to President Jefferson in December 1801 by his friend and frequent correspondent, Robert Patterson, a mathematics professor at the University of Pennsylvania. President Jefferson and Mr. Patterson were both officials at the American Philosophical Society -- a group that promoted scholarly research in the sciences and humanities -- and were enthusiasts of ciphers and other codes, regularly exchanging letters about them.

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University of Pennsylvania ArchivesRobert Patterson

In this message, Mr. Patterson set out to show the president and primary author of the Declaration of Independence what he deemed to be a nearly flawless cipher. "The art of secret writing," or writing in cipher, has "engaged the attention both of the states-man & philosopher for many ages," Mr. Patterson wrote. But, he added, most ciphers fall "far short of perfection."

To Mr. Patterson's view, a perfect code had four properties: It should be adaptable to all languages; it should be simple to learn and memorize; it should be easy to write and to read; and most important of all, "it should be absolutely inscrutable to all unacquainted with the particular key or secret for decyphering."

Mr. Patterson then included in the letter an example of a message in his cipher, one that would be so difficult to decode that it would "defy the united ingenuity of the whole human race," he wrote.

There is no evidence that Jefferson, or anyone else for that matter, ever solved the code. But Jefferson did believe the cipher was so inscrutable that he considered having the State Department use it, and passed it on to the ambassador to France, Robert Livingston.

The cipher finally met its match in Lawren Smithline, a 36-year-old mathematician. Dr. Smithline has a Ph.D. in mathematics and now works professionally with cryptology, or code-breaking, at the Center for Communications Research in Princeton, N.J., a division of the Institute for Defense Analyses.

A couple of years ago, Dr. Smithline's neighbor, who was working on a Jefferson project at Princeton University, told Dr. Smithline of Mr. Patterson's mysterious cipher.

Dr. Smithline, intrigued, decided to take a look. "A problem like this cipher can keep me up at night," he says. After unlocking its hidden message in 2007, Dr. Smithline articulated his puzzle-solving techniques in a recent paper in the magazine American Scientist and also in a profile in Harvard Magazine, his alma mater's alumni journal.

The "Perfect" Cipher?

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The 1801 letter from Robert Patterson to Thomas JeffersonThe code, Mr. Patterson made clear in his letter, was not a simple substitution cipher. That's when you replace one letter of the alphabet with another. The problem with substitution ciphers is that they can be cracked by using what's termed frequency analysis, or studying the number of times that a particular letter occurs in a message. For instance, the letter "e" is the most common letter in English, so if a code is sufficiently long, whatever letter appears most often is likely a substitute for "e."

Because frequency analysis was already well known in the 19th century, cryptographers of the time turned to other techniques. One was called the nomenclator: a catalog of numbers, each standing for a word, syllable, phrase or letter. Mr. Jefferson's correspondence shows that he used several code books of nomenclators. An issue with these tools, according to Mr. Patterson's criteria, is that a nomenclator is too tough to memorize.

Jefferson even wrote about his own ingenious code, a model of which is at his home, Monticello, in Charlottesville, Va. Called the wheel cipher, the device consisted of cylindrical pieces, threaded onto an iron spindle, with letters inscribed on the edge of each wheel in a random order. Users could scramble and unscramble words simply by turning the wheels.

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Congress's Travel Tab Swells 07/03/09California Lays Plans to Issue IOUs to Creditors 07/03/09Wash Wire: Analysis from inside and outside the BeltwayBut Mr. Patterson had a few more tricks up his sleeve. He wrote the message text vertically, in columns from left to right, using no capital letters or spaces. The writing formed a grid, in this case of about 40 lines of some 60 letters each.

Then, Mr. Patterson broke the grid into sections of up to nine lines, numbering each line in the section from one to nine. In the next step, Mr. Patterson transcribed each numbered line to form a new grid, scrambling the order of the numbered lines within each section. Every section, however, repeated the same jumbled order of lines.

The trick to solving the puzzle, as Mr. Patterson explained in his letter, meant knowing the following: the number of lines in each section, the order in which those lines were transcribed and the number of random letters added to each line.

The key to the code consisted of a series of two-digit pairs. The first digit indicated the line number within a section, while the second was the number of letters added to the beginning of that row. For instance, if the key was 58, 71, 33, that meant that Mr. Patterson moved row five to the first line of a section and added eight random letters; then moved row seven to the second line and added one letter, and then moved row three to the third line and added three random letters. Mr. Patterson estimated that the potential combinations to solve the puzzle was "upwards of ninety millions of millions."

THOMAS JEFFERSON

After explaining this in his letter, Mr. Patterson wrote, "I presume the utter impossibility of decyphering will be readily acknowledged."

Undaunted, Dr. Smithline decided to tackle the cipher by analyzing the probability of digraphs, or pairs of letters. Certain pairs of letters, such as "dx," don't exist in English, while some letters almost always appear next to a certain other letter, such as "u" after "q".

To get a sense of language patterns of the era, Dr. Smithline studied the 80,000 letter-characters contained in Jefferson's State of the Union addresses, and counted the frequency of occurrences of "aa," "ab," "ac," through "zz."

Dr. Smithline then made a series of educated guesses, such as the number of rows per section, which two rows belong next to each other, and the number of random letters inserted into a line.

To help vet his guesses, he turned to a tool not available during the 19th century: a computer algorithm. He used what's called "dynamic programming," which solves large problems by breaking puzzles down into smaller pieces and linking together the solutions.

The overall calculations necessary to solve the puzzle were fewer than 100,000, which Dr. Smithline says would be "tedious in the 19th century, but doable."

After about a week of working on the puzzle, the numerical key to Mr. Patterson's cipher emerged -- 13, 34, 57, 65, 22, 78, 49. Using that digital key, he was able to unfurl the cipher's text:

"In Congress, July Fourth, one thousand seven hundred and seventy six. A declaration by the Representatives of the United States of America in Congress assembled. When in the course of human events..."

That, of course, is the beginning -- with a few liberties taken -- to the Declaration of Independence, written at least in part by Jefferson himself. "Patterson played this little joke on Thomas Jefferson," says Dr. Smithline. "And nobody knew until now."

"You see, it's not the blood you spill that gets you what you want, it's the blood you share. Your family, your friendships, your community, these are the most valuable things a man can have." Before Dishonor - Hatebreed

"You see, it's not the blood you spill that gets you what you want, it's the blood you share. Your family, your friendships, your community, these are the most valuable things a man can have." Before Dishonor - Hatebreed

I live in Seattle and my two daily commutes last about 45 minutes. (That's when I'm lucky; sometimes it's more like two hours each.) This has given me an immense amount of time for watching the interesting patterns in the cars. Boredom led me to fantasize about the traffic being like a flowing liquid, with cars acting as giant water molecules. Over many months I slowly realized that this was not just a fantasy. Why had I never noticed all the "traffic fluid dynamics" out there? Once my brain became sensitized to it, I started seeing quite a variety of interesting things occurring. Eventually I started using my car to poke at the flowing traffic. Observation eventually leads to experimentation, no? There are amazing things you can do as an "amateur traffic dynamicist." But first, some basic phenomena.

Planthoppers can be found worldwide and are remarkable insects. They are camouflaged to look like sorrounding leaves and other flora. They move extremely slow on branches so that they don’t attract predator attention, but they have the ability to quickly hop around like grasshoppers for quicker transportation.

In a matter of milliseconds, adult planthoppers can accelerate their leap to roughly 500 Gs. Humans would pass out at this kind of speed and other jumping insects would not be able to keep up.

Scientists say that solar activity is stranger than in a century or more, with the sun producing barely half the number of sunspots as expected and its magnetic poles oddly out of sync.

The sun generates immense magnetic fields as it spins. Sunspots—often broader in diameter than Earth—mark areas of intense magnetic force that brew disruptive solar storms. These storms may abruptly lash their charged particles across millions of miles of space toward Earth, where they can short-circuit satellites, smother cellular signals or damage electrical systems.

Based on historical records, astronomers say the sun this fall ought to be nearing the explosive climax of its approximate 11-year cycle of activity—the so-called solar maximum. But this peak is "a total punk," said Jonathan Cirtain, who works at the National Aeronautics and Space Administration as project scientist for the Japanese satellite Hinode, which maps solar magnetic fields.

"I would say it is the weakest in 200 years," said David Hathaway, head of the solar physics group at NASA's Marshall Space Flight Center in Huntsville, Ala.

Researchers are puzzled. They can't tell if the lull is temporary or the onset of a decades-long decline, which might ease global warming a bit by altering the sun's brightness or the wavelengths of its light.

"There is no scientist alive who has seen a solar cycle as weak as this one," said Andrés Munoz-Jaramillo, who studies the solar-magnetic cycle at the Harvard-Smithsonian Center for Astrophysics in Cambridge, Mass.

To complicate the riddle, the sun also is undergoing one of its oddest magnetic reversals on record.

Normally, the sun's magnetic north and south poles change polarity every 11 years or so. During a magnetic-field reversal, the sun's polar magnetic fields weaken, drop to zero, and then emerge again with the opposite polarity. As far as scientists know, the magnetic shift is notable only because it signals the peak of the solar maximum, said Douglas Biesecker at NASA's Space Environment Center.

But in this cycle, the sun's magnetic poles are out of sync, solar scientists said. The sun's north magnetic pole reversed polarity more than a year ago, so it has the same polarity as the south pole.

"The delay between the two reversals is unusually long," said solar physicist Karel Schrijver at the Lockheed Martin Advanced Technology Center in Palo Alto, Calif.

Scientists said they are puzzled, but not concerned, by the unusual delay. They expect the sun's south pole to change polarity next month, based on current satellite measurements of its shifting magnetic fields.

At the same time, scientists can't explain the scarcity of sunspots. While still turbulent, the sun seems feeble compared with its peak power in previous decades. "It is not just that there are fewer sunspots, but they are less active sunspots," Dr. Schrijver said.(More at the link)